The microbial loop of a naturally acidic bog lake, Grosse Fuchskuhle (Northeastern Germany), that had been artificially divided into 4 basins, was investigated. In the northeast (NE) and southwest (SW) basins, which differ strongly in chemistry and primary production, we conducted intensive studies of the main carbon fluxes through microbial food webs. In the less acidic, NE basin, much higher phytoplankton as well as bacterial biomass and production were found in parallel with negligible numbers of larger zooplankters. Weakly top-down controlled populations of protists were characterized by an exceptionally low numerical proportion of heterotrophic nanoflagellates (HNF) to ciliates (similar to 1.5-3.5). The ciliate community was dominated by a scuticociliate, Cyclidium sp. (>95% of total ciliates), with an estimated grazing rate equal to 46-80% of heterotrophic bacterial production. In contrast, in the more humic, SW basin, both phyto-and bacterioplankton dynamics seemed to be top-down controlled by abundant populations of small fine-filter feeding. cladocerans, Ceriodaphnia quadrangula and Diaphanosoma brachyurum. Consequently, ciliates disappeared from the food web structure of the SW basin, HNF dropped to negligible numbers and bacteria showed very uniform morphology, dominated by small cocci or short rods. Our investigations have shown that the division of the lake into separate compartments can lead to very different microbial food web structures with extreme species compositions.